Skip to Main content Skip to Navigation
Journal articles

Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat

Abstract : Using targeted genetical genomics, a quantitative trait locus (QTL) affecting the initial postmortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) recently was fine-mapped. Thirteen genes were present in the QTL region of approximately 1 Mb. In this study, 10 birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for resequencing. After enrichment for 1 Mb around the QTL region, >500 x coverage for the QTL region in each of the 10 birds was obtained. In total 5056 single-nucleotide polymorphisms (SNPs) were identified for which the genotypes were consistent with one of the QTL genotypes. We used custom tools to identify putative causal mutations in the mapped QTL region from these SNPs. Four nonsynonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B, and E1BTD2). Although these are likely candidate SNPs to explain the QTL effect, 54 additional consensus SNPs were detected within gene-related regions (untranslated regions, splicing sites CpG island, and promoter regions) for the QQ birds and 71 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial postmortem pH value of chicken muscle.
Document type :
Journal articles
Complete list of metadata

Cited literature [21 references]  Display  Hide  Download

https://hal.inrae.fr/hal-02632145
Contributor : Migration Prodinra <>
Submitted on : Wednesday, May 27, 2020 - 10:07:22 AM
Last modification on : Monday, April 19, 2021 - 1:22:48 PM

File

2015_Li_G3 - Genes Genomes Gen...
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Xidan Li, Xiaodong Liu, Javad Mahabadyani Nadaf, Elisabeth Le Bihan-Duval, Cécile Berri, et al.. Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat. G3, Genetics Society of America, 2015, 5 (10), pp.2085 - 2089. ⟨10.1534/g3.115.020552⟩. ⟨hal-02632145⟩

Share

Metrics

Record views

438

Files downloads

49